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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ), 'gf_id' => 'HOM05D001607', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001607' ), 'data_identifier' => 'HOM05D001607', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001607', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '401', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p12270' => 'bna', 'A03p52520' => 'bna', 'Aa31LG6G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3434' => 'aag', 'Actinidia25880' => 'ach', 'Actinidia27741' => 'ach', 'Actinidia28326' => 'ach', 'Actinidia34121' => 'ach', 'Ah.07g207010' => 'amhyb', 'AL7G33300' => 'aly', 'Aqoxy1G00239' => 'aox', 'arahy.Tifrunner.gnm1.ann1.18M8R5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2YSW8E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5K396S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5UA5U0' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7UXB07' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7Y045D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B9FIPF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C6CLGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CMMP9X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GK85WT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HT839T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HZL4S5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8PQ41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L95KH7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M3PRP5' => 'arhy', 'AT4G20850' => 'ath', 'ATR0680G209' => 'atr', 'ATR0680G301' => 'atr', 'Atru.chr1.433' => 'acertr', 'AUR62015965' => 'cqu', 'AUR62021171' => 'cqu', 'BcaC05g27066' => 'bca', 'BcaC09g51300' => 'bca', 'BcaNung04146' => 'bca', 'BcaNung04147' => 'bca', 'BcaNung05068' => 'bca', 'BcaNung05685' => 'bca', 'BcaNung07357' => 'bca', 'BolC1t01419H' => 'bol', 'BolC7t45597H' => 'bol', 'BraA01t01171Z' => 'bra', 'BraA03t14327Z' => 'bra', 'C01p14680' => 'bna', 'C07p50960' => 'bna', 'C09p39310' => 'bna', 'CAN.G307.23' => 'can', 'CAN.G307.24' => 'can', 'CAN.G307.25' => 'can', 'CANSAT21G1423' => 'cansat', 'CARHR227400' => 'chi', 'Carub.0007s2059' => 'cru', 'Ca_05502_v3' => 'car', 'Ca_05504_v3' => 'car', 'Ca_05507_v3' => 'car', 'Ca_10751_v3' => 'car', 'Ca_14559_v3' => 'car', 'Ca_27533_v3' => 'car', 'Ca_27875_v3' => 'car', 'CDE08G0131' => 'cde', 'CDE08G1124' => 'cde', 'Cfa022709' => 'cfa', 'Cfa022711' => 'cfa', 'Cfa022712' => 'cfa', 'Ciclev10004167m.g' => 'ccl', 'CiPaw.03G107800' => 'cil', 'CiPaw.04G071800' => 'cil', 'ClCG00G002810' => 'cla', 'ClCG00G002820' => 'cla', 'ClCG01G004440' => 'cla', 'COL.COLO4_14332' => 'col', 'COL.COLO4_22613' => 'col', 'COL.COLO4_28776' => 'col', 'Cpa.g.sc107.64' => 'cpa', 'Cpa.g.sc107.66' => 'cpa', 'Cre16.g675350' => 'cre', 'CsaV3_5G004660' => 'csa', 'CSS0006239' => 'camsi', 'CSS0006931' => 'camsi', 'CSS0019814' => 'camsi', 'CSS0024839' => 'camsi', 'CSS0037491' => 'camsi', 'DCAR_001509' => 'dca', 'Dinv28425' => 'din', 'Duzib068G0651' => 'dzi', 'Duzib205G1855' => 'dzi', 'ECA233G1901' => 'eca', 'ECA233G5223' => 'eca', 'EL10Ac3g05618' => 'bvu', 'Eucgr.A02778' => 'egr', 'Eucgr.A02780' => 'egr', 'FAN01G0648' => 'fan', 'FAN03G1039' => 'fan', 'FAN03G1056' => 'fan', 'FAN06G1924' => 'fan', 'FAN06G4239' => 'fan', 'FAN10G1529' => 'fan', 'FAN10G2541' => 'fan', 'FvH4_7g29630' => 'fve', 'Glyma.09G137200' => 'gma', 'Glyma.09G137300' => 'gma', 'Glyma.09G137350' => 'gma', 'Glyma.09G137500' => 'gma', 'Glyma.10G109100' => 'gma', 'Glyma.10G234500' => 'gma', 'Glyma.16G182500' => 'gma', 'Gohir.A08G099300' => 'ghi', 'Gohir.A11G010500' => 'ghi', 'Gohir.D08G110708' => 'ghi', 'Gohir.D08G110716' => 'ghi', 'Gohir.D08G110724' => 'ghi', 'Gohir.D11G009700' => 'ghi', 'Gorai.004G118300' => 'gra', 'Gorai.004G118400' => 'gra', 'Gorai.007G011200' => 'gra', 'GSVIVG01020946001' => 'vvi', 'GSVIVG01020947001' => 'vvi', 'GSVIVG01020953001' => 'vvi', 'GSVIVG01020954001' => 'vvi', 'GSVIVG01028926001' => 'vvi', 'GSVIVG01028927001' => 'vvi', 'GSVIVG01028929001' => 'vvi', 'HanXRQChr10g0304171' => 'han', 'Haze_13673' => 'cav', 'Hma1.2p1_1380F.1_g279270' => 'hma', 'HPP92_006560' => 'vpl', 'HPP92_011358' => 'vpl', 'HPP92_011359' => 'vpl', 'Hund04758' => 'sun', 'Hund04843' => 'sun', 'Lalb_Chr02g0141081' => 'lal', 'Lalb_Chr19g0130771' => 'lal', 'Lj1A999G29' => 'lonja', 'Lj2g0000053' => 'lja', 'Lj5g0010480' => 'lja', 'Lsat_1_v5_gn_3_118641' => 'lsa', 'Lsat_1_v5_gn_8_8420' => 'lsa', 'Manes.06G148500' => 'mes', 'Manes.06G148952' => 'mes', 'Mapoly0069s0029' => 'mpo', 'MBI18_g25519_MAGBIO' => 'mbi', 'MD01G1203100' => 'mdo', 'MD07G1272200' => 'mdo', 'MD07G1272600' => 'mdo', 'Medtr0025s0060' => 'mtr', 'Medtr1g101015' => 'mtr', 'Medtr1g101030' => 'mtr', 'MELO3C005470.2' => 'cme', 'MELO3C027008.2' => 'cme', 'MELO3C034501.2' => 'cme', 'Migut.F00330' => 'egut', 'MSTRG.27107' => 'ama', 'Nitab4.5_0000980g0200' => 'nta', 'Nitab4.5_0001842g0120' => 'nta', 'Nitab4.5_0003131g0040' => 'nta', 'Nitab4.5_0005845g0040' => 'nta', 'Nitab4.5_0005845g0050' => 'nta', 'Nn1g01507' => 'nnu', 'Oeu045396.1' => 'oeu', 'Os02g0664300' => 'osa', 'Peaxi162Scf00444g00717' => 'pax', 'Peaxi162Scf00444g00720' => 'pax', 'Peaxi162Scf00444g00722' => 'pax', 'PGR042G0514' => 'pgr', 'PGSC0003DMG400019983' => 'stu', 'Phvul.004G114200' => 'pvu', 'Phvul.007G071600' => 'pvu', 'Potri.012G142200' => 'ptr', 'Potri.015G145300' => 'ptr', 'Pp3c2_32340' => 'ppa', 'Pp3c2_32420' => 'ppa', 'Pp3c7_23000' => 'ppa', 'PRCOL_00005219' => 'pco', 'Prupe.2G295900' => 'ppe', 'Psat0s3405g0040' => 'psa', 'Psat0s3405g0080' => 'psa', 'Psat6g198240' => 'psa', 'PSO478G2555' => 'pso', 'PSO782G3230' => 'pso', 'QL09p013733' => 'qlo', 'QL09p013882' => 'qlo', 'QL93p1997_0001' => 'qlo', 'QL93p2019_0012' => 'qlo', 'RcHm_v2.0_Chr1g0377641' => 'rch', 'RcHm_v2.0_Chr1g0378641' => 'rch', 'RcHm_v2.0_Chr1g0378651' => 'rch', 'Rhsim03G0187200' => 'rsi', 'Rhsim05G0128400' => 'rsi', 'Sabra12G0106800' => 'sbr', 'SalBow4G1573' => 'sbo', 'Sc25g0000580' => 'sci', 'Sed0028131' => 'sed', 'SEGI_09189' => 'sgi', 'SEGI_12683' => 'sgi', 'SEGI_13029' => 'sgi', 'SEGI_31249' => 'sgi', 'SEGI_36427' => 'sgi', 'SGA_v2.0_scaffold44G16733' => 'sas', 'SGA_v2.0_scaffold60G21061' => 'sas', 'SHI01470' => 'shi', 'SHI01866' => 'shi', 'SHI03257' => 'shi', 'SHI07591' => 'shi', 'SHI07622' => 'shi', 'SHI09977' => 'shi', 'SHI12510' => 'shi', 'SHI12514' => 'shi', 'SHI12973' => 'shi', 'SHI13772' => 'shi', 'SHI17153' => 'shi', 'SHI17279' => 'shi', 'SHI17500' => 'shi', 'SHI18583' => 'shi', 'SHI19507' => 'shi', 'SHI19793' => 'shi', 'SHI20615' => 'shi', 'SHI20622' => 'shi', 'SHI27291' => 'shi', 'SHI27311' => 'shi', 'SHI27326' => 'shi', 'SHI28638' => 'shi', 'SHI29350' => 'shi', 'SHI29677' => 'shi', 'SHI29817' => 'shi', 'SHI29818' => 'shi', 'SHI29960' => 'shi', 'SHI31372' => 'shi', 'SHI31542' => 'shi', 'SHI32023' => 'shi', 'SHI32637' => 'shi', 'SHI33308' => 'shi', 'SHI33455' => 'shi', 'SHI34196' => 'shi', 'SHI34197' => 'shi', 'SHI34334' => 'shi', 'SHI34712' => 'shi', 'SHI34874' => 'shi', 'SHI35008' => 'shi', 'SHI35126' => 'shi', 'SHI35171' => 'shi', 'SHI35284' => 'shi', 'SHI35317' => 'shi', 'SHI35771' => 'shi', 'SHI36164' => 'shi', 'SHI36166' => 'shi', 'SHI36350' => 'shi', 'SHI36438' => 'shi', 'SHI36445' => 'shi', 'SHI36760' => 'shi', 'SHI37182' => 'shi', 'SHI37549' => 'shi', 'SHI37689' => 'shi', 'SHI38139' => 'shi', 'SHI38286' => 'shi', 'SHI38321' => 'shi', 'SHI38336' => 'shi', 'SHI38367' => 'shi', 'SHI38909' => 'shi', 'SHI39067' => 'shi', 'SHI39142' => 'shi', 'SHI39452' => 'shi', 'SHI39833' => 'shi', 'SHI39835' => 'shi', 'SHI39897' => 'shi', 'SHI39949' => 'shi', 'SHI40073' => 'shi', 'SHI40439' => 'shi', 'SHI42412' => 'shi', 'SHI42480' => 'shi', 'SHI42704' => 'shi', 'SHI42886' => 'shi', 'SHI43310' => 'shi', 'SHI43595' => 'shi', 'SHI45003' => 'shi', 'SHI45246' => 'shi', 'SHI45657' => 'shi', 'SHI46226' => 'shi', 'SHI47040' => 'shi', 'SHI47121' => 'shi', 'SHI47143' => 'shi', 'SHI47780' => 'shi', 'SHI48479' => 'shi', 'SHI48664' => 'shi', 'SHI48882' => 'shi', 'SHI49096' => 'shi', 'SHI49348' => 'shi', 'SHI49655' => 'shi', 'SHI49988' => 'shi', 'SHI50191' => 'shi', 'SHI50208' => 'shi', 'SHI50291' => 'shi', 'SHI50518' => 'shi', 'SHI50598' => 'shi', 'SHI50611' => 'shi', 'SHI50747' => 'shi', 'SHI50829' => 'shi', 'SHI50834' => 'shi', 'SHI50875' => 'shi', 'SHI50967' => 'shi', 'SHI50996' => 'shi', 'SHI51071' => 'shi', 'SHI51073' => 'shi', 'SHI51100' => 'shi', 'SHI51139' => 'shi', 'SHI51146' => 'shi', 'SHI51257' => 'shi', 'SHI51265' => 'shi', 'SHI51286' => 'shi', 'SHI51314' => 'shi', 'SHI51363' => 'shi', 'SHI51373' => 'shi', 'SHI51393' => 'shi', 'SHI51408' => 'shi', 'SHI51434' => 'shi', 'SHI51445' => 'shi', 'SHI51466' => 'shi', 'SHI51473' => 'shi', 'SHI51475' => 'shi', 'SHI51481' => 'shi', 'SHI51493' => 'shi', 'SHI51502' => 'shi', 'SHI51516' => 'shi', 'SHI51566' => 'shi', 'SHI51575' => 'shi', 'SHI51585' => 'shi', 'SHI51593' => 'shi', 'SHI51594' => 'shi', 'SHI51644' => 'shi', 'SHI51659' => 'shi', 'SHI51682' => 'shi', 'SHI51730' => 'shi', 'SHI51806' => 'shi', 'SHI51824' => 'shi', 'SHI51833' => 'shi', 'SHI51849' => 'shi', 'SHI51913' => 'shi', 'SHI51923' => 'shi', 'SHI51939' => 'shi', 'SHI51959' => 'shi', 'SHI51987' => 'shi', 'SHI52001' => 'shi', 'SHI52005' => 'shi', 'SHI52039' => 'shi', 'SHI52042' => 'shi', 'SHI52078' => 'shi', 'SHI52151' => 'shi', 'SHI52576' => 'shi', 'SHI52599' => 'shi', 'SHI52799' => 'shi', 'SHI52823' => 'shi', 'SHI52825' => 'shi', 'SHI52836' => 'shi', 'SHI52885' => 'shi', 'SHI52897' => 'shi', 'SHI52916' => 'shi', 'SHI53064' => 'shi', 'SHI53240' => 'shi', 'SHI53307' => 'shi', 'SHI53316' => 'shi', 'SHI53323' => 'shi', 'SHI53343' => 'shi', 'SHI53348' => 'shi', 'SHI53468' => 'shi', 'SHI53663' => 'shi', 'SHI53834' => 'shi', 'SHI53902' => 'shi', 'SHI53915' => 'shi', 'SHI53940' => 'shi', 'SHI54036' => 'shi', 'SHI54070' => 'shi', 'SHI54211' => 'shi', 'SHI54252' => 'shi', 'SHI54338' => 'shi', 'SHI55267' => 'shi', 'SMO367G0172' => 'smo', 'Solyc03g025610.3' => 'sly', 'Solyc03g025630.3' => 'sly', 'Sopen00g013600' => 'spe', 'Sopen03g004440' => 'spe', 'Sopen03g004450' => 'spe', 'Sp7g18940' => 'spa', 'TAR375G0166' => 'tar', 'THA.LOC104812206' => 'tha', 'THA.LOC104818559' => 'tha', 'THA.LOC104824854' => 'tha', 'THA.LOC104824860' => 'tha', 'THA.LOC104825607' => 'tha', 'Thecc.03G178600' => 'tca', 'Thhalv10024222m.g' => 'esa', 'TPR.G26981' => 'tpr', 'TPR.G34952' => 'tpr', 'TPR.G8164' => 'tpr', 'TWI39G1280' => 'twi', 'unitig_46.g18793' => 'ugi', 'unitig_46.g18794' => 'ugi', 'vmacro06666' => 'vma', 'vmacro06667' => 'vma', 'VMungo0464G1130' => 'vmu', 'VMungo0720G1584' => 'vmu', 'Zm00001eb223440' => 'zma', 'Zm00001eb249900' => 'zma' ) $gf_id = 'HOM05D001607' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001607' ) $data_identifier = 'HOM05D001607' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 15, 'ath' => (int) 1, 'atr' => (int) 2, 'acertr' => (int) 1, 'cqu' => (int) 2, 'bca' => (int) 7, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 3, 'cansat' => (int) 1, 'chi' => (int) 1, 'cru' => (int) 1, 'car' => (int) 7, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 2, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 5, 'dca' => (int) 1, 'din' => (int) 1, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 7, 'fve' => (int) 1, 'gma' => (int) 7, 'ghi' => (int) 6, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 1, 'cav' => (int) 1, 'hma' => (int) 1, 'vpl' => (int) 3, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 1, 'lja' => (int) 2, 'lsa' => (int) 2, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mdo' => (int) 3, 'mtr' => (int) 3, 'cme' => (int) 3, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 5, 'nnu' => (int) 1, 'oeu' => (int) 1, 'osa' => (int) 1, 'pax' => (int) 3, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 3, 'pso' => (int) 2, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 1, 'sbo' => (int) 1, 'sci' => (int) 1, 'sed' => (int) 1, 'sgi' => (int) 5, 'sas' => (int) 2, 'shi' => (int) 175, 'smo' => (int) 1, 'sly' => (int) 2, 'spe' => (int) 3, 'spa' => (int) 1, 'tar' => (int) 1, 'tha' => (int) 5, 'tca' => (int) 1, 'esa' => (int) 1, 'tpr' => (int) 3, 'twi' => (int) 1, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb249900' $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